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Fig. 4 | Genome Biology

Fig. 4

From: Genome-wide analysis and functional annotation of chromatin-enriched noncoding RNAs in rice during somatic cell regeneration

Fig. 4

Analysis of the regulatory mechanism of che-lincRNAs. A Schematic representation of a cheRNA locus with upstream and downstream coding genes. B Comparison of the Pearson correlation coefficients (PCCs) of the absolute values of the expression of che-lincRNAs and their neighboring genes in input, grouped on the basis of strand and orientation to che-lincRNAs. “Random” represents PCC between the expression of che-lincRNAs and randomly selected mRNAs, and triangles represent the mean value of each group. C Similar to B but grouped by the distance to che-lincRNAs. D Comparison of input (total RNAs) expression (FPKM) of the nearest neighboring genes, grouped based on strand and orientation to che-lincRNAs (as indicated in A) in four tissues. E Similar to D but grouped based on the distance to che-lincRNAs. F Mean ChIP-seq coverage in callas and shoot of H3K4me3, H3K27ac, H3K27me3, and DNase-seq coverage profiles centered around the TSS of the closest genes of callus-specific or shoot-specific enriched che-lincRNAs respectively (mean CPE FPKM ≥ 5). G Consensus motifs in the che-lincRNA transcripts and neighboring gene DNA regions, identified by MEME with default parameters. Relative location was calculated and normalized based on each transcript length, and the density plot was constructed using ggplot2 in R. H GO analysis of neighboring genes of che-lincRNAs from the indicated clusters. The significant GO enrichment results (p < 0.05) were summarized using REVIGO. The aggregate size indicates the significance levels of the GO term, as determined using the Yekutieli test with false discovery rate correction. In B–E, p values were calculated by Wilcoxon Mann-Whitney test, p < 0.05 (*), p < 0.01 (**), p < 0.001 (***)

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